Amycolatopsis acidiphila sp. nov., a moderately acidophilic species isolated from coal mine soil.

Little is known on members of the genus Amycolatopsis inhabiting acidic habitats. In this study, a moderately acidophilic Amycolatopsis strain, designated 2-5T, was isolated from coal mine soil, and subjected to a polyphasic taxonomic characterization. Analysis based on 16S rRNA gene sequences indicated that the strain was most closely related to the type strain of Amycolatopsis bartoniae, sharing 99.30 % similarity, while similarity to all other Amycolatopsis species was less than 97 %. The DNA-DNA relatedness between the new isolate and the type strain of A. bartoniae was 56.5±0.7 %. The optimal pH range of the isolate for growth was 5.5-6.0, but growth also occurred at pH 4.5 and 7.5. The isolate tolerated up to 6 % (w/v) NaCl (optimum, 0 %), and the temperature range for growth was 15-40 °C (optimum, 30 °C). The isolate was able to utilize most substrates tested for sole carbon sources, showing its metabolic versatility. The isolate exhibited antimicrobial activity against Serratia marcescens and weak antifungal activity against Fusarium proliferatum. The chemotaxonomic profiles of strain 2-5T included polar lipids containing phosphatidylethanolamine, phsphatidylmethylethanolamine, phosphatidylglycerol, phosphatidylinositol and phosphatidylinositol dimannosides, fatty acids containing C17 : 1ω6c and iso-C16 : 0 as the major components, MK-9(H4) as the predominant menaquinone, and meso-diaminopimelic acid and arabinose, galactose, glucose and ribose as the diagnostic diamino acid and sugars in the cell wall. The combined phenotypic, chemotaxonomic and genotypic analyses clearly indicated that the isolate merits recognition as represnting a novel species of Amycolatopsis, for which the name Amycolatopsis acidiphila sp. nov. is proposed. The type strain is 2-5T (=KCTC 39523T=JCM 30562T).

Sphingomonas aeria sp. nov. from indoor air of a pharmaceutical environment.

A proteobacterial strain designated R1-3(T) was isolated from indoor air of a pharmaceutical environment. Cells were Gram-stain-negative, oxidase- and catalase-positive, aerobic, motile and rod-shaped. Strain R1-3(T) grew optimally at pH 7, 30 °C and in 0-2 % NaCl on R2A agar. The 16S rRNA gene sequence analysis indicated that strain R1-3(T) belongs to the genus Sphingomonas, and is closely related to Sphingomonas paucimobilis ATCC 29837(T) (98.4 % sequence similarity). However, the DNA-DNA relatedness between the two strains was 43 ± 5 % (reciprocal = 37 ± 3 %), which was well below the suggested level for species distinction. Sphingomonas yabuuchiae GTC868(T) (97.7 % 16S rRNA gene sequence similarity) and Sphingomonas pseudosanguinis G1-2(T) (97.6 %) were also found as distantly related taxa. Strain R1-3(T) was sensitive to most of the tested antibiotics except for erythromycin and streptomycin. The major fatty acid was a summed feature consisting of C18:1 ω7c and/or C18:1 ω6c, and minor proportions of C14:0 2-OH, C16:0 and a summed feature consisting of C16:1 ω7c and/or C16:1 ω6c were also present. The DNA G + C content was 67.2 ± 1.0 mol%. The major polyamines were sym-homospermidine and spermidine. The major polar lipids were phosphatidylglycerol, phosphatidylethanolamine, diphosphatidylglycerol, and minor amounts of a sphingoglycolipid, a phospholipid, an aminoglycolipid and an unidentified lipid were also present. The phenotypic, phylogenetic and chemotaxonomic data not only supported the affiliation of strain R1-3(T) to the genus Sphingomonas, but also distinguished R1-3(T) from related species. On the basis of physiological, chemotaxonomic and phylogenetic evidences, strain R1-3(T) clearly merits recognition as a novel species of Sphingomonas, for which the name Sphingomonas aeria sp. nov. is proposed. The type strain is R1-3(T) (= KCTC 42061(T) = JCM 19859(T)).

Altererythrobacter troitsensis sp. nov., isolated from the sea urchin Strongylocentrotus intermedius.

An aerobic, halotolerant, Gram-negative bacterium was isolated from the sea urchin Strongylocentrotus intermedius and subjected to taxonomic characterization. The strain, designated KMM 6042(T), was rod-shaped, motile and yellow-pigmented. Phylogenetic analysis indicated that the strain was most closely related to the type strain of Altererythrobacter dongtanensis, and the level of 16S rRNA gene sequence similarity between the two was 99.0 %. However, the DNA-DNA relatedness between the two strains was 34.4 ± 7.6 %. Physiological and chemotaxonomic properties clearly distinguished the novel strain from other species of the genus Altererythrobacter. It is thus evident from the phylogenetic and phenotypic analyses that strain KMM 6042(T) merits recognition as a novel species of the genus Altererythrobacter, for which the name Altererythrobacter troitsensis sp. nov. (type strain, KMM 6042(T) = KCTC 12303(T) = JCM 17037(T)) is proposed.

Myroides marinus sp. nov., a member of the family Flavobacteriaceae, isolated from seawater.

A Gram-negative, aerobic, non-motile, yellow-pigmented, rod-shaped bacterium (strain JS-08(T)) isolated from seawater was subjected to a polyphasic taxonomic study. 16S rRNA gene sequence analysis indicated that strain JS-08(T) belongs to the genus Myroides, a member of the phylum Bacteroidetes. Its closest phylogenetic relative was Myroides odoratimimus JCM 7460(T), with which it shared 97.0 % 16S RNA gene sequence similarity. Strain JS-08(T) contained menaquinone-6 (MK-6) as the predominant menaquinone, and the dominant fatty acids were iso-C(15 : 0), iso-C(17 : 0) 3-OH and a summed feature consisting of iso-C(15 : 0) 2-OH and/or C(16 : 1)ω7c. The DNA G+C content of strain JS-08(T) was 34.2 mol%. Based on phenotypic, genotypic and phylogenetic evidence, it is suggested that strain JS-08(T) represents a novel species of the genus Myroides, for which the name Myroides marinus sp. nov. is proposed. The type strain is JS-08(T) ( = KCTC 23023(T)  = JCM 16529(T)).

Hymenobacter yonginensis sp. nov., isolated from a mesotrophic artificial lake.

A non-motile, red-pigmented bacterium, designated strain HMD1010(T), was isolated from an artificial lake located within the campus of Hankuk University of Foreign Studies, Yongin, Korea. A phylogenetic tree based on 16S rRNA gene sequences showed that strain HMD1010(T) formed a lineage within the genus Hymenobacter and was closely related to the type strains of Hymenobacter rigui (96.7 % sequence similarity) and H. gelipurpurascens (95.6 %). The major fatty acids were C(16 : 1)ω5c (21.9 %), summed feature 3 (iso-C(15 : 0) 2-OH and/or C(16 : 1)ω7c; 17.2 %), iso-C(15 : 0) (14.5 %) and summed feature 4 (anteiso-C(17 : 1) B and/or iso-C(17 : 1) I; 11.9 %). The DNA G+C content was 60.4 mol%. On the basis of the evidence presented in this study, strain HMD1010(T) represents a novel species of the genus Hymenobacter, for which the name Hymenobacter yonginensis sp. nov. was proposed. The type strain is HMD1010(T) ( = KCTC 22745(T)  = CECT 7546(T)).

Gramella gaetbulicola sp. nov., a member of the family Flavobacteriaceae isolated from foreshore soil.

A Gram-reaction-negative, yellow-pigmented, gliding, rod-shaped, aerobic bacterium (RA5-111(T)) was isolated from foreshore soil. The taxonomic status of the novel isolate was determined using a polyphasic approach. On the basis of 16S rRNA gene sequence similarities, strain RA5-111(T) could be assigned to the genus Gramella, with sequence similarities of 97.7, 97.3 and 96.2 % to the type strains of Gramella echinicola, Gramella portivictoriae and Gramella marina, respectively. Chemotaxonomic and phenotypic characteristics also supported the affiliation of strain RA5-111(T) with the genus Gramella. The genomic DNA G+C content was 39.1 mol%. The isolate contained MK-6 as the predominant menaquinone, iso-C(15 : 0), iso-C(17 : 0) 3-OH and a summed feature (iso-C(15 : 0) 2-OH and/or C(16 : 1)ω7c) as major fatty acids, and phosphatidylethanolamine and unknown phospholipids as the polar lipids. DNA-DNA relatedness, phenotypic, genotypic and chemotaxonomic data clearly indicate that the isolate represents a novel species of the genus Gramella, for which the name Gramella gaetbulicola sp. nov. is proposed. The type strain is RA5-111(T) ( = KCTC 23022(T) = JCM 16528(T) = NBRC 106272(T)).

Description of Streptomyces neopeptinius sp. nov., an actinobacterium with broad spectrum antifungal activities.

A streptomycete strain producing broad-spectrum antifungal substances was taxonomically characterized. The strain, designated KNF 2047(T) (= SH-09(T) = KCTC 10586BP(T)), was found to form extensively branching aerial and substrate mycelia, and produce spiny-ornamented spores with loose spiral chains. The whole cell hydrolyzates contained major amount of LL-diaminopimelic acid. The major fatty acids of the phospholipids were saturated and branched fatty acids containing 14~17 carbons, and the major isoprenoid quinones were hexa-and octa-hydrogenated menaquinones with 9 isoprene units. The phylogenetic analysis using the 16S rRNA gene indicated that the strain belongs to the genus Streptomyces but forms an independent phyletic line. These results clearly demonstrate that strain KNF2047(T) forms a new center of taxonomic variation within Streptomyces, for which the name Streptomyces neopeptinius sp. nov. is proposed.

Phylogenetic diversity of acidophilic sporoactinobacteria isolated from various soils.

Spore forming actinobacteria (sporoactinobacteria) isolated from soils with an acidic pH in Pinus thunbergii forests and coal mine waste were subjected to taxonomic characterization. For the isolation of acidophilic actinobacteria, acidified starch casein agar (pH adjusted to 4-5) was used. The numbers of actinobacteria growing in acidic media were between 3.2 x 10(4) and 8.0 x 10(6) CFU/g soil. Forty three acidophilic actinobacterial strains were isolated and their 16S rDNA sequences were determined. The isolates were divided into eight distinctive phylogenetic clusters within the variation encompassed by the family Streptomycetaceae. Four clusters among them were assigned to the genus Streptacidiphilus, whereas the remaining four were assigned to Streptomyces. The clusters belonging to either Streptomyces or Streptacidiphilus did not form monophyletic clade. The growth pH profiles indicated that the representative isolates grew best between pH 5 and 6. It is evident from this study that acidity has played a critical role in the differentiation of the family Streptomycetaceae, and also that different mechanisms might have resulted in the evolution of two groups, Streptacidiphilus (strict acidophiles) and neutrotolerant acidophilic Streptomyces. The effect of geographic separation was clearly seen among the Streptacidiphilus isolates, which may be a key factor in speciation of the genus.

Paenibacillus insulae sp. nov., isolated from soil.

A Gram-stain-positive, motile, endospore-forming, and strictly aerobic rod-shaped bacterium designated DS80(T) was isolated from an island soil. The strain DS80(T) grew at temperatures between 15 and 40°C (optimum = 30°C) and at pH values ranging from 5.0 to 9.0 (optimum = 7.0). The phylogenetic analysis based on the comparisons of the 16S rRNA gene sequences showed that the isolate was affiliated to the genus Paenibacillus and was mostly related to Paenibacillus assamensis GPTSA11(T) (with the sequence similarity of 96.33%) and Paenibacillus urinalis 5402403(T)(95.48%). The G+C content of the genomic DNA was 44.0 mol% and the major fatty acids were anteiso-C15:0, iso-C15:0, iso-C16:0, and C16:1 ω11c. Strain DS80(T) contained MK-7 as the major menaquinone, and phosphatidylglycerol, phosphatidylethanolamine, and diphosphatidylglycerol as the major polar lipids. The peptidoglycan contained a major amount of meso-diaminopimelic acid. The chemotaxonomic profile of strain DS80(T) was consistent with that of Paenibacillus. However, the phenotypic properties clearly separated the strain from other species of the genus. Accordingly, a new species, Paenibacillus insulae sp. nov., is proposed (type strain =DS80(T) =JCM 17278(T) =KCTC 13833(T)).

Diversity and physiological properties of root endophytic actinobacteria in native herbaceous plants of Korea.

Endophytic actinobacterial diversity in the native herbaceous plant species of Korea was analyzed using a culture-based approach. Sixty one actinobacterial strains were isolated, and assigned to 15 genera based on 16S rRNA gene analysis. The members of the genus Streptomyces comprised 45.9% of the total isolates, followed by Micromonospora (18.8%), Rhodococcus (6.6%), Microbispora (4.9%), and Micrococcus (4.9%). Other minor constituents included members of Microbacterium, Streptacidiphilus, Arthrobacter, Dietzia, Kitasatospora, Herbiconiux, Mycobacterium, Nocardia, Rathayibacter, and Tsukamurella. Among the isolates, 65.6% exhibited at least one hydrolytic enzyme activity out of four, and 45.9% exhibited antagonistic activity against at least one fungal pathogen out of five, thus demonstrating that endophytic actinobacteria can be an important source of bioactive compounds. Notably, most strains of Streptomyces proved active for both enzymatic and antagonistic activities.

Four new species of Chryseobacterium from the rhizosphere of coastal sand dune plants, Chryseobacterium elymi sp. nov., Chryseobacterium hagamense sp. nov., Chryseobacterium lathyri sp. nov. and Chryseobacterium rhizosphaerae sp. nov.

The taxonomic positions of five Gram-negative, non-spore-forming and non-motile bacterial strains isolated from the rhizosphere of sand dune plants were examined using a polyphasic approach. The analysis of the 16S rRNA gene sequence indicated that all of the isolates fell into four distinct phylogenetic clusters belonging to the genus Chryseobacterium of the family Flavobacteriaceae. The 16S rRNA gene sequence similarities of isolates to mostly related type strains of Chryseobacterium ranged from 97.5% to 98.5%. All strains contained MK-6 as the predominant menaquinone, and iso-C(15:0), iso-C(17:0) 3-OH and a summed feature of iso-C(15:0) 2-OH and/or C(16:1) omega7c as the dominant fatty acids. Combined phenotypic, genotypic and chemotaxonomic data supported that they represented four novel species in the genus Chryseobacterium, for which the names Chryseobacterium hagamense sp. nov. (type strain RHA2-9(T)=KCTC 22545(T)=NBRC 105253(T)), Chryseobacterium elymi sp. nov. (type strain RHA3-1(T)=KCTC 22547(T)=NBRC 105251(T)), Chryseobacterium lathyri sp. nov. (type strain RBA2-6(T)=KCTC 22544(T)=NBRC 105250(T)), and Chryseobacterium rhizosphaerae sp. nov. (type strain RSB3-1(T)=KCTC 22548(T)=NBRC 105248(T)) are proposed.

Streptacidiphilus anmyonensis sp. nov., Streptacidiphilus rugosus sp. nov. and Streptacidiphilus melanogenes sp. nov., acidophilic actinobacteria isolated from Pinus soils.

The taxonomic positions of 22 spore-forming, extensively branched actinobacteria isolated from Pinus soils were examined using a polyphasic approach. Analysis of the 16S rRNA gene sequences indicated that all of the isolates fell into three distinctive phylogenetic clusters within the genus Streptacidiphilus of the family Streptomycetaceae, and also that Streptacidiphilus jiangxiensis was the species closest to the three phyloclusters, with 16S rRNA gene sequence similarities ranging from 98.0 to 99.2 %. However, the low DNA-DNA relatedness values between representatives of the three clusters and S. jiangxiensis clearly differentiated them from one another. Representative isolates were also found to have chemotaxonomic features typical of the genus Streptacidiphilus and were distinguishable from all established species of Streptacidiphilus on the basis of a combination of phenotypic properties. It is evident from this study that each of the three phyloclusters should be equated with three novel Streptacidiphilus species, for which the following names are proposed: Streptacidiphilus anmyonensis sp. nov. (type strain AM11(T) =NBRC 103185(T) =KCTC 19278(T)), Streptacidiphilus rugosus sp. nov. (type strain AM16(T) =NBRC 103186(T) =KCTC 19279(T)) and Streptacidiphilus melanogenes sp. nov. (type strain SB-B34(T) =NBRC 103184(T) =KCTC 19280(T)).